add workflows

.github/workflows/R-CMD-check-hard-push.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# NOTE: This workflow only directly installs "hard" dependencies, i.e. Depends,
+# Imports, and LinkingTo dependencies. Notably, Suggests dependencies are never
+# installed, with the exception of testthat, knitr, and rmarkdown. The cache is
+# never used to avoid accidentally restoring a cache containing a suggested
+# dependency.
+on:
+  push:
+    branches:
+      - master
+
+name: R-CMD-check-hard
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: windows-latest, r: "release" }
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      # Always try to use the latest pandoc version
+      # https://github.com/jgm/pandoc/releases
+      - uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: "2.19.2"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          dependencies: '"hard"'
+          cache: false
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::knitr
+            any::rmarkdown
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/R-CMD-check-hard.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# NOTE: This workflow only directly installs "hard" dependencies, i.e. Depends,
+# Imports, and LinkingTo dependencies. Notably, Suggests dependencies are never
+# installed, with the exception of testthat, knitr, and rmarkdown. The cache is
+# never used to avoid accidentally restoring a cache containing a suggested
+# dependency.
+on:
+  pull_request:
+    branches:
+      - master
+
+name: R-CMD-check-hard
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, r: "devel" }
+          - { os: windows-latest, r: "release" }
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      # Always try to use the latest pandoc version
+      # https://github.com/jgm/pandoc/releases
+      - uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: "2.19.2"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          dependencies: '"hard"'
+          cache: false
+          extra-packages: |
+            any::rcmdcheck
+            any::testthat
+            any::knitr
+            any::rmarkdown
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/R-CMD-check-push.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+
+on:
+  push:
+    branches:
+      - master
+
+name: R-CMD-check
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }}) ${{ matrix.config.locale }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          ##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+          ##                              IMPORTANT                                   ##
+          ##                                                                          ##
+          ##             Checks are deliberately not run on R-devel.                  ##
+          ##  This is because they are already run in `R-CMD-check-strict` workflow.  ##
+          ##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+          - { os: windows-latest, r: "devel" }
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      _R_CHECK_CRAN_INCOMING_: false
+      _R_CHECK_FORCE_SUGGESTS_: false
+
+    steps:
+      # - name: Set locale
+      #   if: matrix.config.locale == 'zh_CN.UTF-8'
+      #   run: |
+      #     sudo locale-gen zh_CN.UTF-8
+      #     echo "LC_ALL=zh_CN.UTF-8" >> $GITHUB_ENV
+
+      - name: Set locale
+        if: matrix.config.locale == 'en_US'
+        run: |
+          sudo locale-gen en_US
+          echo "LC_ALL=en_US" >> $GITHUB_ENV
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: "3.1"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: "release"
+          use-public-rspm: true
+
+      - name: Install packages from source
+        run: |
+          install.packages(c("Matrix", "TMB"), type = "source")
+        shell: Rscript {0}
+
+      # TODO: Check which of the ignore conditions are still relevant given the
+      # current suggested dependencies and the minimum supported R version.
+      # Update if anything out of date or not needed anymore.
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          extra-packages: |
+            any::rcmdcheck
+            any::BH
+            TMB=?ignore-before-r=100.0.0
+            Matrix=?ignore-before-r=100.0.0
+            glmmTMB=?ignore-before-r=100.0.0
+            epiR=?ignore-before-r=4.0.0
+            gam=?ignore-before-r=4.0.0
+            gdtools=?ignore-before-r=4.0.0
+            fastICA=?ignore-before-r=4.0.0
+            metafor=?ignore-before-r=4.0.0
+            panelr=?ignore-before-r=4.0.0
+            jtools=?ignore-before-r=4.0.0
+            mmrm=?ignore-before-r=4.0.0
+            rsvd=?ignore-before-r=4.0.0
+            sparsepca=?ignore-before-r=4.0.0
+            qqconf=?ignore-before-r=4.0.0
+            qqplotr=?ignore-before-r=4.0.0
+            ape=?ignore-before-r=4.1.0
+            car=?ignore-before-r=4.1.0
+            drc=?ignore-before-r=4.1.0
+            EGAnet=?ignore-before-r=4.1.0
+            ggpubr=?ignore-before-r=4.1.0
+            rstatix=?ignore-before-r=4.1.0
+            PROreg=?ignore-before-r=4.1.0
+            FactoMineR=?ignore-before-r=4.3.0
+            factoextra=?ignore-before-r=4.3.0
+            sjstats=?ignore-before-r=4.3.0
+            nestedLogit=?ignore-before-r=4.3.0
+            estimability=?ignore-before-r=4.3.0
+            emmeans=?ignore-before-r=4.3.0
+            effects=?ignore-before-r=4.3.0
+            rmcorr=?ignore-before-r=4.1.0
+            randomForest=?ignore-before-r=4.1.0
+            MuMIn=?ignore-before-r=4.2.0
+            pbkrtest=?ignore-before-r=4.1.0
+            afex=?ignore-before-r=4.1.0
+            car=?ignore-before-r=4.1.0
+            ivreg=?ignore-before-r=4.1.0
+            AER=?ignore-before-r=4.1.0
+          needs: check
+
+      # install *after* other deps to avoid FreeADFunObject error
+      - name: Install glmmTMB from source
+        run: |
+          install.packages(c("MatrixModels", "glmmTMB"), type = "source")
+        shell: Rscript {0}
+
+      # Don't error on "note" because if any of the suggested packages are not available
+      # for a given R version, this generates a NOTE causing unnecessary build failure
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          error-on: '"warning"'
+          upload-snapshots: true

.github/workflows/check-all-examples.yaml

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+# Make sure all examples run successfully, even the ones that are not supposed
+# to be run or tested on CRAN machines by default.
+#
+# The examples that fail should use
+#  - `if (FALSE) { ... }` (if example is included only for illustrative purposes)
+#  - `try({ ... })` (if the intent is to show the error)
+#
+# This workflow helps find such failing examples that need to be modified.
+on:
+  pull_request:
+    branches: [master]
+
+name: check-all-examples
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-all-examples:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          #r-version: "devel"
+          use-public-rspm: true
+
+      - name: Install packages from source
+        run: |
+          install.packages(c("Matrix", "TMB"), type = "source")
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          #cache-version: 2
+          pak-version: devel
+          extra-packages: |
+            TMB=?ignore-before-r=100.0.0
+            Matrix=?ignore-before-r=100.0.0
+            any::devtools
+            local::.
+      - name: Run examples
+        run: |
+          options(crayon.enabled = TRUE, warn = 2L)
+          devtools::run_examples(run_dontrun = TRUE, run_donttest = TRUE, document = FALSE)
+        shell: Rscript {0}

.github/workflows/check-link-rot.yaml

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+on:
+  pull_request:
+    branches: [master]
+
+name: check-link-rot
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+jobs:
+  check-link-rot:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: "3.1"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          #r-version: "devel"
+          http-user-agent: "release"
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: devel
+          dependencies: '"hard"'
+          extra-packages: |
+            any::rcmdcheck
+            any::urlchecker
+      - name: Run URL checker
+        run: |
+          options(crayon.enabled = TRUE)
+          rotten_links <- urlchecker::url_check(progress = FALSE)
+          print(rotten_links)
+          if (length(rotten_links$URL) > 0L) {
+            cli::cli_abort("Some URLs are outdated and need to be updated.")
+          }
+        shell: Rscript {0}